SMTL ID : 4og4.1

Human menin with bound inhibitor MIV-3S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 1 residues within 4Å: Chain A: R.317 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.317

1 x 2VK: 4-(3-{4-[(S)-cyclopentyl(hydroxy)phenylmethyl]piperidin-1-yl}propoxy)benzonitrile(Non-covalent)

2VK.2: 15 residues within 4Å: Chain A: S.140, S.163, E.164, H.166, F.223, C.226, A.227, M.263, Y.304, M.307, Y.308, G.311, W.326, E.348 Ligands: TBF.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.223, A:A.227, A:M.307

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 3 residues within 4Å: Chain A: Y.346, F.350, H.406 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.346

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 6 residues within 4Å: Chain A: W.111, N.112, L.114, S.115, K.120, W.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.112, A:L.114, A:K.120

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 3 residues within 4Å: Chain A: Y.253, D.254, G.256 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.254, A:E.259, A:E.259 PEG.10: 4 residues within 4Å: Chain A: H.51, F.52, V.55, N.56 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.51, A:N.56 Water bridges: A:H.51

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 2 residues within 4Å: Chain A: P.17, R.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.19 DMS.7: 6 residues within 4Å: Chain A: V.170, G.175, E.176, T.178, Y.212, R.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.214 DMS.8: 5 residues within 4Å: Chain A: R.317, V.319, R.320, S.375, A.376 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.319, A:R.320 DMS.9: 3 residues within 4Å: Chain A: F.48, F.52, P.64 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.65 pi-Cation interactions: A:F.52

1 x TBF: TERT-BUTYL FORMATE(Non-functional Binders)

TBF.11: 1 residues within 4Å: Ligands: 2VK.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, S. et al., High-Affinity Small-Molecule Inhibitors of the Menin-Mixed Lineage Leukemia (MLL) Interaction Closely Mimic a Natural Protein-Protein Interaction. J.Med.Chem. (2014)

Release Date

2014-03-05

Peptides

Menin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Menin

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